Intro to FreeSurfer Jargon

voxelsurfacevolumevertexsurface-basedreconcortical, subcorticalparcellation/segmentationregistration, morph, deform, transforms

(computing vs. resampling)

What FreeSurfer Does… FreeSurfer creates

computerized models of the brain from MRI data.

Input:T1-weighted (MPRAGE,SPGR)

1mm3 resolution(.dcm)

Output:Segmented & parcellated conformed

volume(.mgz)

Intro to FreeSurfer Jargon

voxel

Intro to FreeSurfer Jargon

surface

Intro to FreeSurfer Jargon

surface

Intro to FreeSurfer Jargon

vertex

Intro to FreeSurfer Jargon

vertex

Volume = Surface Area x Thickness

Recon

“recon your data”…short for reconstruction

…cortical surface reconstruction…shows up in command

recon-all

Recon

Volumes

orig.mgz T1.mgz brainmask.mgz wm.mgz filled.mgz(Subcortical Mass)

Cortical vs. Subcortical GM

coronalsagittal

subcortical gm

cortical gm

Cortical vs. Subcortical GM

coronalsagittal

subcortical gm

Parcellation vs. Segmentation

(subcortical) segmentation

(cortical) parcellation